Variant report

Variant	rs12878099
Chromosome Location	chr14:78061233-78061234
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:78059041..78061902-chr14:78067196..78069981,2	K562	blood:
2	chr14:78060053..78062225-chr14:78085684..78087947,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10132804	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10139421	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873310	0.81[ASN][1000 genomes]
rs11159282	0.81[ASN][1000 genomes]
rs11159285	0.80[ASN][1000 genomes]
rs12432127	0.80[ASN][1000 genomes]
rs12435993	0.89[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12586560	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs12880698	0.84[ASN][1000 genomes]
rs12881338	0.94[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs12881530	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs12898009	0.82[CHB][hapmap]
rs4899664	0.81[ASN][1000 genomes]
rs4903619	0.80[ASN][1000 genomes]
rs56812919	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7149026	0.80[ASN][1000 genomes]
rs7153483	0.96[ASN][1000 genomes]
rs7155602	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832835	chr14:77906706-78095207	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1053810	chr14:77987871-78148320	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1051554	chr14:78004196-78122980	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78013200-78066200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:78021800-78068400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:78021800-78071600	Weak transcription	Colon Smooth Muscle	Colon
4	chr14:78042400-78066600	Weak transcription	Fetal Brain Female	brain
5	chr14:78042600-78061800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr14:78043800-78061800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr14:78047400-78070000	Weak transcription	Fetal Brain Male	brain
8	chr14:78048000-78061400	Weak transcription	Fetal Intestine Small	intestine
9	chr14:78048200-78067200	Weak transcription	Hela-S3	cervix
10	chr14:78049400-78066400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr14:78051400-78061400	Weak transcription	Esophagus	oesophagus
12	chr14:78051400-78061800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr14:78051400-78061800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr14:78051400-78066200	Weak transcription	Pancreas	Pancrea
15	chr14:78051400-78070200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr14:78051600-78063000	Weak transcription	Left Ventricle	heart
17	chr14:78051600-78072600	Weak transcription	Psoas Muscle	Psoas
18	chr14:78052000-78061800	Weak transcription	Brain Anterior Caudate	brain
19	chr14:78052200-78062200	Weak transcription	Brain Angular Gyrus	brain
20	chr14:78052600-78061800	Weak transcription	Ovary	ovary
21	chr14:78055000-78081600	Weak transcription	Right Ventricle	heart
22	chr14:78056600-78072800	Weak transcription	Placenta	Placenta
23	chr14:78056800-78070000	Weak transcription	Gastric	stomach
24	chr14:78057000-78064000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr14:78057000-78065000	Weak transcription	Lung	lung
26	chr14:78057400-78070000	Weak transcription	Spleen	Spleen
27	chr14:78057600-78081400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr14:78057800-78061400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr14:78057800-78061600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr14:78057800-78065000	Weak transcription	Small Intestine	intestine
31	chr14:78058000-78063600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr14:78058800-78063800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr14:78059000-78061400	Genic enhancers	HSMM	muscle
34	chr14:78059000-78063800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr14:78059000-78065800	Weak transcription	Colonic Mucosa	Colon
36	chr14:78060000-78061400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr14:78060000-78061400	Weak transcription	NHLF	lung
38	chr14:78060000-78062800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr14:78060200-78061400	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr14:78060200-78061400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr14:78060200-78066800	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr14:78060200-78069400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr14:78060400-78061400	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr14:78060400-78061400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr14:78060400-78061400	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr14:78060400-78061400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr14:78060400-78061600	Weak transcription	Brain Hippocampus Middle	brain
48	chr14:78060400-78063400	Strong transcription	HMEC	breast
49	chr14:78060400-78065000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr14:78060400-78065400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links